Haven't tested all helium recipes (just the ones I've unlocked in my playthrough), but regarding the green, red, and blue circuit alternative recipes, I believe the helium usage is bugged for reds and blues. with green circuits, no matter how much productivity, the amount of helium in = the amount of helium out. This is what leads me to believe the behavior for the other 2 is a bug and not a feature. With red circuits, which theoretically should be the same as greens (helium in = helium out), even just the innate +50% productivity from EM plants (no modules required) creates a positive feedback loop of helium, generating it from nothing. This seems unintended. Blue circuits also will generate infinite helium with no modules required.

1 other thing: I noticed an older (closed) thread mentioning the Helium from Beryllium recipe is meant to consume 10 iron beryllium plates instead of 100. That thread is marked as fixed, but my game still shows 100. I assumed this was intended until I saw that thread while looking to see if someone had already reported the above issue. I'm happy to make a 2nd thread if someone wants me to.

update: realized the fixes for this are not backported to factorio 2.0, and appear to only be available for factorio 2.1, whoops.

Had extra time, backported a few bug fixes to factorio version 2.0 for this mod under the version name 0.2.8.

the productivity thing with helium should be fixed and helium itself shouldn't take 100 beryllium plates to make
(I couldn't directly test the mod as that would have required me to downgrade my game to 2.0 so if there are any major issues with this version, please report them)

I unfortunately will not be able to test this as this was the thing that pushed me to rip the bandaid off and update to 2.1 (something Ive been meaning to do for a while) so hopefully your fix works lol.